GetRelM: Matrix with Pairwise Relationships

Description

Generate a matrix or 3D array with all pairwise relationships from a pedigree or dataframe with pairs.

Usage

GetRelM(
  Pedigree = NULL,
  Pairs = NULL,
  GenBack = 1,
  patmat = FALSE,
  directed = TRUE,
  Return = "Matrix",
  Pairs_suffix = "?"
)

Value

If Return='Matrix', an N x N square matrix, with N equal to the number of rows in Pedigree (after running

PedPolish) or the number of unique individuals in

Pairs. If Return='Array', an N x N x R array is returned, with R, the number of different relationships, determined by GenBack

and patmat.

The following abbreviations are used within the returned Matrix, or as names of the 3rd dimension in the Array or of the List:

S: Self
M: Mother
P: Father
MP: Mother or Father (patmat=FALSE)
O: Offspring
FS: Full sibling
MHS: Maternal half-sibling
PHS: Paternal half-sibling
XHS: other half-sibling (hermaphrodites)
HS: half-sibling (patmat=FALSE)
MGM: Maternal grandmother
MGF: Maternal grandfather
PGM: Paternal grandmother
PGF: Paternal grandfather
GP: Grandparent (patmat=FALSE)
GO: Grand-offspring
FA: Full avuncular; maternal or paternal aunt or uncle.
FN: Full nephew/niece
HA: Half avuncular
HN: Half nephew/niece
DFC1: Double full first cousin
FC1: Full first cousin
U: Unrelated (or otherwise related)

Arguments

Pedigree: dataframe with columns id - dam - sire.
Pairs: dataframe with columns ID1 - ID2 - Rel, e.g. as returned by GetMaybeRel. Combining Pedigree and Pairs works best if the relationships are coded as listed below.
GenBack: number of generations back to consider; 1 returns parent-offspring and sibling relationships, 2 also returns grand-parental, avuncular and first cousins.
patmat: logical, distinguish between paternal versus maternal relative pairs? For avuncular pairs, the distinction is never made.
directed: logical, distinguish between e.g. ID1=offspring, ID2=mother ('M') and ID1=mother, ID2=offspring ('O')? Defaults to TRUE; if FALSE both are are scored as 'PO', as are father-offspring pairs, and all grandparent-- grand-offspring pairs are scored as 'GPO', and avuncular pairs as 'FNA' and 'HNA'. Not (currently) compatible with patmat. When Return='List', each pair is included twice (as ID1-ID2 & ID2-ID1)
Return: 'Matrix', 'Array', or 'List'. 'Matrix' returns an N x N matrix with the closest relationship between each pair. 'Array' returns an N x N x R array with for each of the R considered relationships whether it exists between the pair (1) or not (0). See Details below. 'List' returns a list with for each of the R considered relationships a 2-column matrix with the IDs of the pairs having such a relationship. The size of the list (in Mb) is much smaller than for the matrix or array, and this is therefore the only format suitable for pedigrees with many thousands of individuals. If Pairs is specified, the only possible return type is 'Matrix'.
Pairs_suffix: symbol added to the relationship abbreviations derived from Pairs, when both Pedigree and Pairs are provided. Can be an empty string.

Details

Double relationships are ignored when Return='Matrix', but not when Return='Array'. For example, when A and B are both mother-offspring and paternal siblings (A mated with her father to produce B), only the mother-offspring relationship will be indicated when Return='Matrix'.

Note that full siblings are the exception to this rule: in the Array they will be indicated as 'FS' only, and not as 'MHS' or 'PHS'. Similarly, full avuncular pairs are not indicated as 'HA'. Double half-avuncular relationships are indicated as both FA and HA.

When Pairs is provided, GenBack and patmat are ignored, and no check is performed if the abbreviations are compatible with other functions.

Examples

Run this code

Rel.griffin <- GetRelM(Ped_griffin, directed=FALSE)  # few categories
Rel.griffin <- GetRelM(Ped_griffin, patmat=TRUE, GenBack=2)  # many cat.
table(as.vector(Rel.griffin))
# turning matrix into vector first makes table() much faster
PlotRelPairs(Rel.griffin)